Battery voltage reads about .75 lower than my voltmeter reads at the breaker.

I haven't checked the voltage cal on mine, but imagine that if anything is correct, this would be.  When you say at the breaker, do you mean the breaker that feeds the EM-2?  If you have one of electric Bob's essential buss setups, with a diode between the two busses, that will drop your voltage close to what you're seeing.

The RWS air temp sensors (I have 3) all read 6-8 degrees lower than actual air temp (75F at the time).  I expect these should be accurate.

If you're referring to the 3 wire sensors, Tracy said they were always very accurate by definition, assuming they're wired correctly.  However, my OAT temp was reading about 15 degrees low.  I ended up zeroing out the sensor offset, and got the OAT reading within about 4 degrees of what I was reading with the Radio Shack thermometer.  That's where I left it for now.   

 The J-type TCs read right on air temp. The K-type TCs are about 5-7 low at ambient temps, that doesn’t really matter.
Oil and coolant temps were somewhat off, but I adjusted calibration factors to get them about right.  But didn’t quite know whether to change ‘Low end offset’ or the ‘Sensor offset’.  I assume for the VDO sensors the scale factors are correct. 

My temps were pretty good on the latest EM-2 software that I just installed.  Pressures were the problem, and I'm not sure why they were so significantly off from the previous version.  The sensors I'm using are still the same ones recommended, but I was able to calibrate them reasonably well.  For example, my fuel pressure was 42 psi before, but came up 59 on the new sw.  Oil on the new sw was ringing the bell at about 88 psi, when in actuality, it's about 75 psi. 

I wish I could give you a clear definition of sensor offset vs. low end offset, but I'm not sure I can.  All the settings seem to interact, which can be a bit frustrating to calibrate.  One of the most powerful features of the EM-2 is it's ability to adapt to any number of different sensors, but this comes at a price of being responsible for it's calibration.  The best we can hope for is to have certain known sensors precalibrated, and I'm sure Tracy will perfect this at some point.   As I said, my temps are pretty OK, but not the pressures.   

The more general question on temp calibration is, short of taking out the sensor and putting it in boiling water, what’s a good (read easy) way to get another reference point at something like operating temp?

I got a spare of every type of sensor that I'm using, which gives me the ability to calibrate everything, without pulling any of the actual sensors out of the engine.  The caveat here is that all sensors are somewhat different, but I'm betting any two of the same brand and type of sensor are close enough for our purposes. 

The best test I can think of for water temp is boiling water, though it's hard to keep it at 212 degrees for any length of time.  I have a microwave in the hanger, and can heat water that way.  I also have a calibrated thermocouple that I use to measure the water at the same time I put the sensor in it for calibration.  That way, you can calibrate to the temp of the thermocouple.